Entering edit mode
Hi! While running TSS enrichment score for scATAC-seq, I found it took me so long time to compute and ended up terminating the process because my Mac was overheating. I am using Mac (M2) but have R for Mac Intel because there were some of the packages from Bioconductor that I couldn't install using R for Mac M1. Could anyone let me know how to improve computing time for TSS enrichment?
Code should be placed in three backticks as shown below
pbmc <- TSSEnrichment (object = pbmc, fast = FALSE)
Extracting TSS positions
Finding + strand cut sites
[W::hts_idx_load2] The index file is older than the data file: <file path>
sessionInfo( )
Had the same problem. Tried running with
fast = TRUEand could see how it should complete. I'm on M1 mac using R for apple silicon and most stuff seems to work ok.I'm guessing its a memory issue but afraid I gave up.
Hi Taeim,
I am facing a similar issue, a call to TSSEnrichment takes ~6 hours with a Multiome dataset of ~9K cells. IIRC, this function did not take this long to execute in previous analyses I've done. Did you ever manage to find a working solution, or did you just end up dealing with the long computation time?